Diff of the two buildlogs: -- --- b1/build.log 2024-05-01 07:47:33.787735081 +0000 +++ b2/build.log 2024-05-01 07:53:49.591669042 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Apr 30 19:35:40 -12 2024 -I: pbuilder-time-stamp: 1714548940 +I: Current time: Wed Jun 4 04:10:49 +14 2025 +I: pbuilder-time-stamp: 1748959849 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -33,52 +33,84 @@ dpkg-source: info: applying fix_linking.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3458207/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1027586/tmp/hooks/D01_modify_environment starting +debug: Running on codethink01-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jun 3 14:10 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/1027586/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1027586/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='48be44fa9882457b923b78174ba79d03' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='3458207' - PS1='# ' - PS2='> ' + INVOCATION_ID=173533f6eca84bbb8f40bf1b4366cc36 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1027586 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.LMGp7gzT/pbuilderrc_mShQ --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.LMGp7gzT/b1 --logfile b1/build.log mothur_1.48.0-2.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.LMGp7gzT/pbuilderrc_rCse --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.LMGp7gzT/b2 --logfile b2/build.log mothur_1.48.0-2.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 27 07:42 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3458207/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 3 14:05 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1027586/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -171,7 +203,7 @@ Get: 47 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-4 [157 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libreadline-dev arm64 8.2-4 [153 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3.1 [915 kB] -Fetched 52.4 MB in 0s (140 MB/s) +Fetched 52.4 MB in 0s (194 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package readline-common. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19735 files and directories currently installed.) @@ -388,7 +420,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/mothur-1.48.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../mothur_1.48.0-2_source.changes +I: user script /srv/workspace/pbuilder/1027586/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/1027586/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/mothur-1.48.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../mothur_1.48.0-2_source.changes dpkg-buildpackage: info: source package mothur dpkg-buildpackage: info: source version 1.48.0-2 dpkg-buildpackage: info: source distribution unstable @@ -552,13 +588,6 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/cmdargs.o source/clearcut/cmdargs.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/distclearcut.o source/clearcut/distclearcut.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/dmat.o source/clearcut/dmat.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/fasta.o source/clearcut/fasta.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/getopt_long.o source/clearcut/getopt_long.cpp -source/clearcut/dmat.cpp: In function 'DMAT* NJ_parse_distance_matrix(NJ_ARGS*)': -source/clearcut/dmat.cpp:456:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 456 | fscanf(fp, "%ld\n", &dmat->ntaxa); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/aligncheckcommand.o source/commands/aligncheckcommand.cpp source/clearcut/distclearcut.cpp: In function 'DMAT* NJ_compute_dmat(NJ_ARGS*, NJ_alignment*)': source/clearcut/distclearcut.cpp:155:41: warning: 'char* __builtin_strncat(char*, const char*, long unsigned int)' specified bound depends on the length of the source argument [-Wstringop-overflow=] 155 | *dmat->taxaname[i] = '\0'; strncat(dmat->taxaname[i], alignment->titles[i], strlen(alignment->titles[i])+1); @@ -566,6 +595,13 @@ source/clearcut/distclearcut.cpp:155:89: note: length computed here 155 | *dmat->taxaname[i] = '\0'; strncat(dmat->taxaname[i], alignment->titles[i], strlen(alignment->titles[i])+1); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/fasta.o source/clearcut/fasta.cpp +source/clearcut/dmat.cpp: In function 'DMAT* NJ_parse_distance_matrix(NJ_ARGS*)': +source/clearcut/dmat.cpp:456:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 456 | fscanf(fp, "%ld\n", &dmat->ntaxa); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/clearcut/getopt_long.o source/clearcut/getopt_long.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/aligncheckcommand.o source/commands/aligncheckcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/aligncommand.o source/commands/aligncommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/alignmusclecommand.o source/commands/alignmusclecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/amovacommand.o source/commands/amovacommand.cpp @@ -573,11 +609,11 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/binsequencecommand.o source/commands/binsequencecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/biominfocommand.o source/commands/biominfocommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimerabellerophoncommand.o source/commands/chimerabellerophoncommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeraccodecommand.o source/commands/chimeraccodecommand.cpp source/commands/alignmusclecommand.cpp: In member function 'void AlignMuscleCommand::wrapperFunction()': source/commands/alignmusclecommand.cpp:297:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 297 | system(commandString.c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeraccodecommand.o source/commands/chimeraccodecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeracheckcommand.o source/commands/chimeracheckcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimeraperseuscommand.o source/commands/chimeraperseuscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/chimerapintailcommand.o source/commands/chimerapintailcommand.cpp @@ -589,21 +625,21 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/classifyseqscommand.o source/commands/classifyseqscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/classifysvmsharedcommand.o source/commands/classifysvmsharedcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/classifytreecommand.o source/commands/classifytreecommand.cpp -source/commands/chimeravsearchcommand.cpp: In function 'void driver(vsearchData*)': -source/commands/chimeravsearchcommand.cpp:412:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 412 | system(commandString.c_str()); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clearcutcommand.o source/commands/clearcutcommand.cpp source/commands/chimerauchimecommand.cpp: In function 'int driver(uchimeData*)': source/commands/chimerauchimecommand.cpp:517:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 517 | system(commandString.c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clearcutcommand.o source/commands/clearcutcommand.cpp +source/commands/chimeravsearchcommand.cpp: In function 'void driver(vsearchData*)': +source/commands/chimeravsearchcommand.cpp:412:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 412 | system(commandString.c_str()); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clustercommand.o source/commands/clustercommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clusterdoturcommand.o source/commands/clusterdoturcommand.cpp source/commands/clustercommand.cpp: In member function 'int ClusterCommand::vsearchDriver(std::string, std::string, std::string)': source/commands/clustercommand.cpp:542:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 542 | system(commandString.c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clusterdoturcommand.o source/commands/clusterdoturcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clusterfitcommand.o source/commands/clusterfitcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clusterfragmentscommand.o source/commands/clusterfragmentscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/clustersplitcommand.o source/commands/clustersplitcommand.cpp @@ -624,11 +660,11 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/deuniquetreecommand.o source/commands/deuniquetreecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/distancecommand.o source/commands/distancecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/distsharedcommand.o source/commands/distsharedcommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/diversityestimatorcommand.o source/commands/diversityestimatorcommand.cpp source/commands/distancecommand.cpp: In member function 'virtual int DistanceCommand::execute()': source/commands/distancecommand.cpp:323:31: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 323 | system(("gzip -v " + outputFile).c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/diversityestimatorcommand.o source/commands/diversityestimatorcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/fastaqinfocommand.o source/commands/fastaqinfocommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/filterseqscommand.o source/commands/filterseqscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/filtersharedcommand.o source/commands/filtersharedcommand.cpp @@ -666,11 +702,11 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makefilecommand.o source/commands/makefilecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makegroupcommand.o source/commands/makegroupcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makelefsecommand.o source/commands/makelefsecommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makelookupcommand.o source/commands/makelookupcommand.cpp source/commands/makefilecommand.cpp: In member function 'int MakeFileCommand::fillAccnosFile(std::string)': source/commands/makefilecommand.cpp:354:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 354 | system(findCommand.c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makelookupcommand.o source/commands/makelookupcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/makesharedcommand.o source/commands/makesharedcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mantelcommand.o source/commands/mantelcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/mergecountcommand.o source/commands/mergecountcommand.cpp @@ -691,12 +727,12 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pairwiseseqscommand.o source/commands/pairwiseseqscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/parsimonycommand.o source/commands/parsimonycommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pcacommand.o source/commands/pcacommand.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pcoacommand.o source/commands/pcoacommand.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pcrseqscommand.o source/commands/pcrseqscommand.cpp source/commands/pairwiseseqscommand.cpp: In member function 'virtual int PairwiseSeqsCommand::execute()': source/commands/pairwiseseqscommand.cpp:339:19: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 339 | system(("gzip -v " + outputFile).c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pcoacommand.o source/commands/pcoacommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/pcrseqscommand.o source/commands/pcrseqscommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/phylodiversitycommand.o source/commands/phylodiversitycommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/phylotypecommand.o source/commands/phylotypecommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/preclustercommand.o source/commands/preclustercommand.cpp @@ -732,11 +768,11 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/sracommand.o source/commands/sracommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/srainfocommand.o source/commands/srainfocommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/subsamplecommand.o source/commands/subsamplecommand.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/summarycommand.o source/commands/summarycommand.cpp source/commands/srainfocommand.cpp: In member function 'void SRAInfoCommand::runSystemCommand(std::string)': source/commands/srainfocommand.cpp:487:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 487 | system(inputString.c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/summarycommand.o source/commands/summarycommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/summaryqualcommand.o source/commands/summaryqualcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/summarysharedcommand.o source/commands/summarysharedcommand.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/commands/summarytaxcommand.o source/commands/summarytaxcommand.cpp @@ -876,6 +912,8 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/validparameter.o source/validparameter.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/venn.o source/venn.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/vsearchfileparser.o source/vsearchfileparser.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/weightedlinkage.o source/weightedlinkage.cpp +g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/wilcox.o source/wilcox.cpp source/utils.cpp: In member function 'bool Utils::findTool(std::string&, std::string&, std::vector >&, std::vector > >)': source/utils.cpp:952:19: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 952 | system(versionTestCommand.c_str()); @@ -884,8 +922,6 @@ source/utils.cpp:1514:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1514 | system(command.c_str()); | ~~~~~~^~~~~~~~~~~~~~~~~ -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/weightedlinkage.o source/weightedlinkage.cpp -g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/mothur-1.48.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -O3 -std=c++11 -pthread -DVERSION="\"1.48.0\"" -DRELEASE_DATE="\"5/20/22\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/wilcox.o source/wilcox.cpp cd source/uchime_src && export CXX=g++ && make clean && make && mv uchime ../../ && cd .. make[3]: Entering directory '/build/reproducible-path/mothur-1.48.0/source/uchime_src' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. @@ -1057,12 +1093,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/1027586/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1027586/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/3458207 and its subdirectories -I: Current time: Tue Apr 30 19:47:32 -12 2024 -I: pbuilder-time-stamp: 1714549652 +I: removing directory /srv/workspace/pbuilder/1027586 and its subdirectories +I: Current time: Wed Jun 4 04:16:48 +14 2025 +I: pbuilder-time-stamp: 1748960208